Search Results (63)

Diaphorencyrtus aligarhensis parasitizes the Asian citrus psyllid (ACP), Diaphorina citri, the primary insect vector responsible for transmitting Huanglongbing (HLB), a severe citrus disease. Screening of appropriate reference genes is a critical prerequisite for reliable RT-qPCR analysis, which is essential for investigating the functions of target genes in D. aligarhensis across diverse experimental conditions. However, to date, no validated reference genes have been reported for this species. This study assessed seven housekeeping genes in D. aligarhensis under six conditions (developmental stage, body tissue, population, temperature, diet, and starvation) using five stability algorithms (geNorm, BestKeeper, NormFinder, RefFinder, and ∆Ct). The results identified the most suitable reference genes for specific experimental conditions: EIF5A and RPL32 for the developmental stage; RPL13 and H3 for population comparisons; RPS6 and GAPDH for different feeding diets; RPL32 and RPS6 for starvation; RPL7A and RPS6 for different body tissues (head, thorax, abdomen) and temperature gradients (5 °C, 15 °C, 25 °C, 35 °C). Furthermore, the expression profiles of HSP70 were markedly different when normalized to the most versus the least stable reference genes across body tissues, diets, starvation durations, and temperatures. Our findings establish the first set of RT-qPCR reference genes for D. aligarhensis, providing a useful foundation for functional genomics research on this biological control agent. Full article

Phytoplasmas are obligate intracellular parasitic bacteria that infect over 1000 plant species globally, causing devastating diseases characterized by yellowing, witches’ broom, phyllody, and significant yield losses in economically important crops. The unculturable nature of these pathogens has historically hindered their study; however, advances in molecular biology and genomics have substantially accelerated progress over the past two decades. This review provides a comprehensive overview of current knowledge on phytoplasma diseases and control technologies. In terms of taxonomy, phytoplasmas are currently classified into 37 16Sr groups with over 150 subgroups based on 16S rRNA gene analysis, and approximately 50 ‘Candidatus Phytoplasma’ species have been formally named. Genomic studies have revealed that phytoplasmas possess highly reduced genomes (530–1350 kb) lacking many essential metabolic pathways, reflecting their obligate parasitic lifestyle. Regarding pathogenesis, secreted effector proteins such as SAP (Secreted Aster Yellows Witches’ Broom Protein), TENGU (tengu-su inducer), and SWP (Secreted Wheat Blue Dwarf Protein) manipulate plant hormone signaling and developmental processes, leading to characteristic disease symptoms. Detection technologies have evolved from traditional microscopy to molecular methods, including nested PCR, real-time quantitative PCR, loop-mediated isothermal amplification (LAMP), and CRISPR/Cas-based systems (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein), with AI-based image recognition and remote sensing emerging as promising tools for large-scale field monitoring. Integrated management strategies encompassing agricultural practices, insect vector control, biological control agents, induced resistance, and breeding for resistance are discussed. Finally, future research directions, including functional genomics, microbiome-based approaches, and precision agriculture technologies, are highlighted. This review aims to provide researchers and practitioners with a systematic reference for understanding phytoplasma biology and developing effective disease management strategies. Full article

Background/Objectives: Chromosomal inversions play an important role in the evolution of insects by forming genetic barriers between closely related species and facilitating local adaptation. Polymorphic inversions in malaria mosquitoes of the Maculipennis subgroup have been studied for over 50 years, yet the evolutionary ancestry of the gene orders remains unknown. In this study, we mapped the genes flanking the breakpoints of two polymorphic X-chromosome inversions in the cryptic species Anopheles messeae and Anopheles daciae of the Maculipennis subgroup. Methods: We used an iterative mapping approach to define the breakpoint regions, selecting flanking markers based on the genome assembly of the reference species, Anopheles atroparvus. To identify the ancestral X chromosomal arrangement in An. messeae and An. daciae, we developed and implemented the genomic inversion calculator (GIC), which uses greedy heuristics to determine the shortest evolutionary scenario of rearrangements. Results: Our knowledge of the relative genomic positions of the inversion breakpoints in An. daciae and An. messeae enabled us to use the An. atroparvus genome as an outgroup and the GIC tool to show that the X0 and X2 arrangements emerged independently along the evolutionary lineages of An. daciae and An. messeae, respectively, based on the X1 arrangement. Conclusions: These results refine the structure and boundaries of the X chromosome rearrangements and reconstruct the sequence of evolutionary events in the cryptic complex An. messeae–An. daciae, demonstrating that the X1 arrangement is ancestral. This study lays the groundwork for analyzing the molecular organization of breakpoints, the mechanisms of inversion formation, and their role in speciation. Full article

Soybean production is a cornerstone of Brazilian agriculture but is heavily threatened by insect pests such as the soybean looper Chrysodeixis includens, capable of reducing yields by up to 70% if uncontrolled. Reliance on chemical insecticides is increasingly unsustainable due to environmental impacts and resistance, highlighting the need for eco-friendly alternatives. The alphabaculovirus Chrysodeixis includens nucleopolyhedrovirus (ChinNPV) is an important biocontrol agent largely used in Brazilian fields because of its host specificity and safety, although its persistence is limited by ultraviolet (UV) sensitivity. Here, we characterize two ChinNPV isolates, CNPSo-168 (C168) and Tabatinga (Tb), using genomic and phenotypic analyses. Whole-genome sequencing revealed circular dsDNA genomes of 139,290 bp (154 ORFs) for C168 and 139,131 bp (153 ORFs) for Tb, both encoding the 38 baculovirus core genes and sharing >98.9% identity with reference genomes. Comparative genomics identified 431 SNPs, including 132 nonsynonymous changes in structural, regulatory, and infection-related genes. At low concentrations, C168 showed an approximately 2-fold lower LC₅₀ than Tb (higher potency), while both achieved near-complete mortality within 8 days at higher concentrations. This greater potency at lower concentrations reinforces the efficacy-based rationale for selecting isolate C168 for biocontrol applications. Infection reduced larval growth, pupation, and adult emergence, often with developmental impairments. Despite genetic differences, both isolates were highly UV-sensitive, and formulation tests indicated that titanium dioxide combined with kaolin conferred partial protection. These results provide insights into ChinNPV diversity and support its development as a sustainable tool for soybean pest management. Full article

Propsilocerus akamusi (Tokunaga, 1938) larvae serve as key bioindicators for water quality assessment. This study identifies optimal reference genes for RT-qPCR under diverse experimental conditions. Fifteen candidate genes commonly employed in other insect species were selected, candidate genes commonly used in other insect species. Homologous genes were identified in the P. akamusi genome through sequence alignment with their Drosophila melanogaster counterparts. Expression stability across developmental stages, body parts, temperature variations, and deltamethrin/nickel chloride exposures was systematically evaluated using geNorm, NormFinder, BestKeeper, and ΔCt methods. RPL32 exhibited the highest expression stability across different body parts of adults under varying temperature conditions, and RPS11 and RPL8 showed the greatest stability across developmental stages and in larvae exposed to different temperatures. Furthermore, under nickel chloride and deltamethrin treatments, RPS11 and RPL8 maintained the highest expression stability. The results indicated that the expression stability of reference genes varied under different conditions. Among different body parts of adults, RPL32 and RPL4 exhibited the most stable expression. Across different developmental stages, RPS11 and RPL8 performed best in terms of expression stability. Under different temperature treatments, RPL32 and RPL4 remained stable in adults, while RPS11 and RPL8 showed the greatest stability in larvae. Similarly, under nickel chloride and deltamethrin treatments, RPS11 and RPL8 demonstrated the most stable expression in larvae. Through the above research, we can advance ecosystem-impact insights and bolster environmental protection and water quality monitoring. Full article

The greenbug aphid (Schizaphis graminum (Rondani)) is a major pest of wheat and an important vector of wheat viruses. An RNA-seq study was conducted to investigate the microbial effects of two greenbug genotypes, the presence or absence of cereal yellow dwarf virus, and the condition of the wheat host over a 20-day time course of unrestricted greenbug feeding. Messenger RNA reads were mapped to ca. 47,000 bacterial, 1218 archaeal, 14,165 viral, 571 fungal, and 94 protozoan reference or representative genomes, plus greenbug itself and its wheat host. Taxon counts were analyzed with QIIME2 and DESeq2. Distinct early (days 1 through 10) and late (days 15 and 20) communities differed in the abundance of typical enteric genera (Shigella, Escherichia, Citrobacter), which declined in the late community, while the ratio of microbial to greenbug read counts declined 50% and diversity measures increased. The nearly universal aphid endosymbiont, Buchnera aphidicola, accounted for less than 25% of the read counts in both communities. There were 302 differentially expressed (populated) genera with respect to early and late dates, while 25 genera differed between the greenbug genotypes and nine differed between carrier and virus-free greenbugs. The late community was likely responding to starvation as the wheat host succumbed to aphid feeding. Our results add to basic knowledge about aphid microbiomes and offer an attractive alternative method to assess insect microbiomes. Full article

The insect order Lepidoptera contains many species that are considered to be agricultural pests. Specific double-stranded RNA-degrading enzymes in some moth species decrease the efficiency of RNA interference (RNAi). RNAi refers to the efficient and specific degradation of homologous mRNA induced by highly conserved, double-stranded RNA during evolution. The dsRNase enzymes can specifically recognize exogenous dsRNA, and bind to and degrade dsRNA, resulting in the inability of dsRNA to play its role. Although dsRNases play an important role in dsRNA degradation, there has been limited research on these enzymes. In this study, we successfully identified four genes related to dsRNases (named SeRNase1, SeRNase2, SeRNase3 and SeRNase4) from the genome of Spodoptera exigua. To overcome the rapid degradation of dsRNA in the midgut of S. exigua, we combined nanotechnology with biology and developed a new strategy to administer RNAi to insect pests. This binding block directed contact between the dsRNA and SeRNases to improve the efficiency of RNAi in suppressing gene expression. We demonstrate the potential of using nanotechnology to provide a novel RNAi delivery method for pest control. Full article

Glycoside hydrolase family 18 (GH18) proteins can hydrolyze the β-1,4-glycosidic bonds of chitin, which is a common structure component of insect exoskeletons and fungal cell walls. In this study, 36 GH18 genes were identified and subjected to bioinformatic analysis based on the genomic data of Glycine max. They were distributed in 16 out of 20 tested soybean chromosomes. According to the amino acid sequences, they can be further divided into five subclades. Class III chitinases (22 members) and class V chitinases (6 members) are the major two subclades. The amino acid size of soybean GH18 proteins ranges from 173 amino acids (aa) to 820 aa and the molecular weight ranges from 19.46 kDa to 91.01 kDa. From an evolutionary perspective, soybean GH18 genes are closely related to Medicago (17 collinear loci with soybean) and Lotus (23 collinear loci with soybean). Promoter analysis revealed that GH18 genes could be induced by environmental stress, hormones, and embryo development. GmGH18-15, GmGH18-24, and GmGH18-33 were screened out due to their nodulation specific expression and further verified by RT-qPCR. These results provide an elaborate reference for the further characterization of specific GH18 genes, especially during nodule formation in soybean. Full article

Improving the efficiency of germplasm innovation has always been the aim of rice breeders. Traditional hybrid breeding methods for variety selection rarely meet the practical needs of rice production. The emergence of genome-editing technologies, such as CRISPR/Cas9, provides a new approach to the genetic improvement of crops such as rice. The number of published scientific papers related to “gene editing” and “CRISPR/Cas9” retrievable on websites both from China and other countries exhibited an increasing trend, year by year, from 2014 to 2023. Research related to gene editing in rice accounts for 33.4% and 12.3% of all the literature on gene editing published in China and other countries, respectively, much higher than that on maize and wheat. This article reviews recent research on CRISPR/Cas9 gene-editing technology in rice, especially germplasm innovation and genetic improvement of commercially promoted varieties with improved traits such as disease, insect, and herbicide resistance, salt tolerance, quality, nutrition, and safety. The aim is to provide a reference for the precise and efficient development of new rice cultivars that meet market demand. Full article

Genome sequences contain the fundamental genetic information that largely determines the biology of a species. Over the past 20 years, advancements in high-throughput sequencing technologies and bioinformatics tools have matured, facilitating genome assembly and ushering in the telomere-to-telomere (T2T) era. Bombyx mori is renowned as a silk-producing insect and serves as an important model organism extensively studied across various fields of biology. In this study, we present the first assembled T2T genome by integrating HiFi, ultra-long ONT, NGS, and Hi-C data. This assembly comprises 450,267,439 base pairs from 28 chromosomes and includes annotations for a total of 18,253 protein-coding genes. A completeness evaluation revealed that 99.1% of conserved single-copy genes were included, as determined by a BUSCO analysis. Furthermore, the consensus quality (QV) assessed through Merqury was recorded at 59.88. The proportion of repeat sequence achieved 60.77%, marking it as the highest reported value for B. mori to date. In comparison to previously published genomes, our assembly offers a more complete and higher quality representation, particularly concerning highly homologous tandem regions such as telomeres, rDNA clusters, and Gr family regions. Furthermore, our extensive experience in genome assembly, including sample preparation experience and assembly strategies to reduce complexity, will provide valuable references for other species aiming to achieve their own T2T genome assemblies. Full article

Loreto virus (LORV) is an insect-specific virus classified into the proposed taxon Negevirus. It was originally described in Iquitos, Peru, in 1977. Here, we describe three novel LORV genomes obtained from the isolates of three pooled samples of Trichoprosopon digitatum, Aedes (Ochlerotatus) fulvus, and Limatus durhamii collected in Ilhéus—Bahia, 2014. Samples were submitted to RNA sequencing on the Illumina platform to recover the LORV genome. The genomes presented, on average, 81.5% nucleotide identity and 92.6% global amino acid identity with the LORV reference genome (NC_034158). Subsequently, phylogenetic analysis was performed based on a multiple sequence alignment of the concatenated amino acid sequences predicted for the three ORFs of the Negevirus genomes, and the target sequences were clustered within the LORV clade. The taxon Negevirus is in constant expansion of its species content and host range. New data about insect specific negeviruses are important for virus evolution studies, along with those approaching interactions with the hosts and their influence in the transmission of arboviruses. Also, the assessment of these data may allow the development of biologic control strategies for arboviral vectors. This is the original report of the identification of LORV in Brazil, infecting three Culicidae species hosts native to the Atlantic Forest biome. Full article

The use of CpGV strains as the basis for bioinsecticides is an effective and safe way to control Cydia pomonella. The research is aimed at the identification and study of new CpGV strains. Objects of identification and bioinformatic analysis: 18 CpGV strains. Sequencing was carried out on a NextSeq550. Genome assembly and annotation were carried out using Spades, Samtools 1.9, MinYS, Pilon, Gfinisher, Quast, and Prokka. Comparative genomic analysis was carried out in relation to the reference genome present in the «Madex Tween» strain-producer (biological standard) according to the average nucleotide identity (ANI) criterion. The presence/absence of IAP, cathepsin, MMP, and chitinase in the genetic sequences of the strains was determined using simply phylogeny. Entomopathogenic activity was assessed against C. pomonella according to the criterion of biological efficacy. Thus, molecular genetic identification revealed that 18 CpGV strains belong to a genus of Betabaculovirus. For all the strains under study ANI values of 99% or more were obtained, and the presence of the cathepsin, chitinase, IAP, and MMP genes was noted. The strains BZR GV 1, BZR GV 3, BZR GV 7, BZR GV 10, and BZR GV L-8 showed the maximum biological efficacy: 100% on the 15th day of observation. Strains BZR GV 4, BZR GV 8, and BZR GV 13 showed efficacy at the level of the «Madex Tween» preparation: 89.5% on the 15th day of observation. The strains with the highest mortality rate of the host insect were identified: BZR GV 9, BZR GV 10, BZR GV L-6, and BZR GV L-8. Full article

Rice is a staple crop in sub-Saharan Africa, and it is mostly produced by Asian cultivars of Oryza sativa that were introduced to the continent around the fifteenth or sixteenth century. O. glaberrima, the native African rice, has also been planted due to its valuable traits of insect and drought tolerance. Due to competition and resistance evolution, weedy rice has evolved from O. sativa and O. glaberrima, posing an increasing threat to rice production. This paper provides an overview of current knowledge on the introduction and domestication history of cultivated rice in Africa, as well as the genetic properties of African weedy rice that invades paddy fields. Recent developments in genome sequencing have made it possible to uncover findings about O. glaberrima’s population structure, stress resilience genes, and domestication bottleneck. Future rice genomic research in Africa should prioritize producing more high-quality reference genomes, quantifying the impact of crop–wild hybridization, elucidating weed adaptation mechanisms through resequencing, and establishing a connection between genomic variation and stress tolerance phenotypes to accelerate breeding efforts. Full article

Population replacement refers to the process by which a wild-type population of insect pests is replaced by a population possessing modified traits or abilities. Effective population replacement necessitates a gene drive system capable of spreading desired genes within natural populations, operating under principles akin to super-Mendelian inheritance. Consequently, releasing a small number of genetically edited insects could potentially achieve population control objectives. Currently, several gene drive approaches are under exploration, including the newly adapted CRISPR-Cas genome editing system. Multiple studies are investigating methods to engineer pests that are incapable of causing crop damage or transmitting vector-borne diseases, with several notable successful examples documented. This review summarizes the recent advancements of the CRISPR-Cas system in the realm of population replacement and provides insights into research methodologies, testing protocols, and implementation strategies for gene drive techniques. The review also discusses emerging trends and prospects for establishing genetic tools in pest management. Full article

Cydia pomonella granulovirus is a natural pathogen for Cydia pomonella that is used as a biocontrol agent of insect populations. The study of granulovirus virulence is of particular interest since the development of resistance in natural populations of C. pomonella has been observed during the long-term use of the Mexican isolate CpGV. In our study, we present the genomes of 18 CpGV strains endemic to southern Russia and from Kazakhstan, as well as a strain included in the commercial preparation “Madex Twin”, which were sequenced and analyzed. We performed comparative genomic analysis using several tools. From comparisons at the level of genes and protein products that are involved in the infection process of virosis, synonymous and missense substitution variants have been identified. The average nucleotide identity has demonstrated a high similarity with other granulovirus genomes of different geographic origins. Whole-genome alignment of the 18 genomes relative to the reference revealed regions of low similarity. Analysis of gene repertoire variation has shown that BZR GV 4, BZR GV 6, and BZR GV L-7 strains have been the closest in gene content to the commercial “Madex Twin” strain. We have confirmed two deletions using read depth coverage data in regions lacking genes shown by homology analysis for granuloviruses BZR GV L-4 and BZR GV L-6; however, they are not related to the known genes causing viral pathogenicity. Thus, we have isolated novel CpGV strains and analyzed their potential as strains producing highly effective bioinsecticides against C. pomonella. Full article